Biological research has mainly been focused on proteins for a very long time until interest in nucleic acids has caught up. Still, after RNA was identified as an intermediate product of gene expression, the lack of high-throughput technologies and computational approaches delayed our understanding of the importance and complexity of the regulation of the gene expression at the transcriptional level. In recent years, a wealth of sequencing and computational techniques have been developed to unravel the complex universe of transcriptional regulation of gene expression, therefore opening a field of computational RNA biology and bioinformatics, which, by far, earned an invaluable place in modern RNA biology.

Transcription is carried out by RNA polymerases, which synthetize RNA molecules on the DNA template. Numerous proteins and protein complexes associated with RNA polymerases immediately engage the nascent transcripts allowing their maturation via intron splicing and deposition of chemical modifications. Newly synthesized transcripts are both modified externally (via 5´ end capping and 3´ end polyA tail attachment) and, in more particular contexts, internally (e.g., with m⁶A, pseudouridine, m⁵C, etc). In the present thesis,I summarized the projects about both external (cap-proximal) and internal (mainly m⁶A) RNA modifications I have been involved in as computational biologist.